lindenb / jvarkitLinks
Java utilities for Bioinformatics
☆513Updated 3 weeks ago
Alternatives and similar repositories for jvarkit
Users that are interested in jvarkit are comparing it to the libraries listed below
Sorting:
- DELLY2: Structural variant discovery by integrated paired-end and split-read analysis☆499Updated last month
- Transcript assembly and quantification for RNA-Seq☆475Updated this week
- Plot structural variant signals from many BAMs and CRAMs☆557Updated last year
- A tool to map bisulfite converted sequence reads and determine cytosine methylation states☆439Updated 4 months ago
- Count bases in BAM/CRAM files☆322Updated 3 years ago
- Graph-based alignment (Hierarchical Graph FM index)☆518Updated 3 months ago
- This Snakemake pipeline implements the GATK best-practices workflow☆262Updated 2 years ago
- Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms☆406Updated 4 months ago
- RSEM: accurate quantification of gene and isoform expression from RNA-Seq data☆455Updated last year
- BEDOPS: high-performance genomic feature operations☆356Updated 8 months ago
- Tools to process and analyze deep sequencing data.☆750Updated 5 months ago
- ☆297Updated 2 weeks ago
- annotate a VCF with other VCFs/BEDs/tabixed files☆391Updated 4 months ago
- Structural variant and indel caller for mapped sequencing data☆456Updated 2 months ago
- GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more☆447Updated last year
- Miscellaneous collection of Python and R scripts for processing Iso-Seq data☆278Updated 2 years ago
- Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing☆529Updated last week
- Tools for working with genomic and high throughput sequencing data.☆350Updated last week
- Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/☆549Updated last week
- A One-Click System for Analyzing Loop-Resolution Hi-C Experiments☆472Updated 3 months ago
- The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants☆515Updated 3 weeks ago
- RTG Tools: Utilities for accurate VCF comparison and manipulation☆329Updated 7 months ago
- Tools for working with SAM/BAM data☆599Updated last year
- Strelka2 germline and somatic small variant caller☆389Updated 4 years ago
- A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…☆536Updated 3 months ago
- Fast and accurate gene fusion detection from RNA-Seq data☆257Updated 3 months ago
- Documentation for the ANNOVAR software☆245Updated 5 months ago
- Customizable workflows based on snakemake and python for the analysis of NGS data☆395Updated last week
- Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.☆395Updated last month
- Bayesian haplotype-based genetic polymorphism discovery and genotyping.☆858Updated 6 months ago